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De novo Whole-Genome Assembly of the 10-Gigabase Fokienia Hodginsii Genome to Reveal Differential Epigenetic Events Between Callus and Xylem.
Rong, Jundong; Zheng, Yushan; Zhang, Zeyu; Zhang, Jun; Gu, Yuying; Hua, Tian; Zhao, Mengna; Fan, Lili; Deng, Zhiwen; Pan, Yanmei; Li, Bingjun; Chen, Liguang; He, Tianyou; Chen, Lingyan; Ye, Jing; Zhang, Hangxiao; Gu, Lianfeng.
Afiliação
  • Rong J; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Zheng Y; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Zhang Z; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Zhang J; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Gu Y; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Hua T; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Zhao M; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Fan L; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Deng Z; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Pan Y; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Li B; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Chen L; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • He T; College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Chen L; College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Ye J; College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Zhang H; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
  • Gu L; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Adv Sci (Weinh) ; : e2402644, 2024 Sep 04.
Article em En | MEDLINE | ID: mdl-39229940
ABSTRACT
Fokienia hodginsii (F. hodginsii), belonging to the genus Fokienia of the Cupressaceae. F. hodginsii has significant application value due to its wood properties and great research value in evolutionary studies as a gymnosperm. However, the genome of F. hodginsii remains unknown due to the large size of gymnosperms genome. Pacific Bioscience sequencing, Hi-C mapping, whole-genome Bisulfite Sequencing (BS-Seq), long-read isoform sequencing (Iso-Seq), direct RNA sequencing (DRS), quantitative proteomics, and metabonomics analysis are employed to facilitate genome assembly, gene annotation, and investigation into epigenetic mechanisms. In this study, the 10G F. hodginsii genome is assembled into 11 chromosomes. Furthermore, 50 521 protein-coding genes are annotated and determined that 65% of F. hodginsii genome comprises repetitive sequences. It is discovered that transposable element (TE)-including introns is associated with higher expression. The DNA methylome of F. hodginsii reveals that xylem has a higher DNA methylation level compared to callus. Moreover, DRS reveals the significant alterations in RNA full-length ratio, which potentially associated with poly(A) length (PAL) and alternative polyadenylation (APA). Finally, the morphology measurement and metabonomics analysis revealed the difference of 14 cultivars. In summary, the genomes and epigenetics datasets provide a molecular basis for callus formation in the gymnosperm family.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: Adv Sci (Weinh) Ano de publicação: 2024 Tipo de documento: Article País de afiliação: China País de publicação: Alemanha
Texto completo
Adicionar na Minha BVS
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: Adv Sci (Weinh) Ano de publicação: 2024 Tipo de documento: Article País de afiliação: China País de publicação: Alemanha